My favorite modern Zelda weapon has to be the Skull Hammer from Wind Waker. I'm not entirely sure why, but I seem to have an attachment to the hammers of Zelda, and the overall design of the Skull Hammer was actually rather nice. I liked that - much like in A Link to the Past - it allowed you to hit in stakes and rather heavy switches on the ground. Aside from its usual use, it was also very handy in killing enemies. Despite the fact that it took a bit of time to send flying towards the ground, I not only enjoyed Link's animation - raising it over his head and pounding it down - but I also liked how the bokoblins looked when you hit them with the Skull Hammer; flattened and then exploded seconds later.
Overall, it was an efficient item with its own personal ability, but it also acted as a makeshift melee weapon. Wind Waker definitely wouldn't have been as good for me had I not had that weapon.